ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods

MISFITS: Evaluating the Goodness of Fit between a Phylogenetic Model and an Alignment

(2010) Minh Anh Thi Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

(2010) Liat Shavit Grievink et al.   SYSTEMATIC BIOLOGY

General Heterotachy and Distance Method Adjustments

(2009) J. Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

(2009) Bryan Kolaczkowski et al.   PLoS One

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

(2008) Liat Shavit Grievink et al.   BMC EVOLUTIONARY BIOLOGY

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

(2008) S. Kumar et al.   BRIEFINGS IN BIOINFORMATICS

A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy

(2008) Bryan Kolaczkowski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Errors in Ancient DNA Caused by Postmortem Degradation

(2008) L. M. Mateiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories

(2008) A. Rambaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of single substitutions on multiple sequence alignments

(2008) S. Klaere et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

(2008) M. Pagel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY